Persistence of Escherichia coli O157:H7 in major leafy green producing soils

Survival behavior of six enterotoxigenic Escherichia coli strains in soil and biochar-amended soils

Some Escherichia coli serotypes are important human pathogens causing diarrhea or in some cases, life threatening diseases. E. coli is also a typical indicator microorganism, routinely used for assessing the microbiological quality of water especially to indicate fecal contamination. The soil is a sink and route of transmission to water and food resources and it is thus important to understand the survival of enterotoxigenic E. coli strains in soil. This study monitored the survival of six E. coli strains in sandy and loam soil. Furthermore, since biochar is a commonly used soil conditioner, the study investigated the impact of biochar amendment (15%) on the survival of the E. coli strains in (biochar-amended) sandy and loam soils. Addition of biochar affected the physicochemical properties of both soils, altering potassium levels, calcium, magnesium, sodium as well as levels of other metal ions. It increased the organic matter of loam soil from 44 g/dm³ to 52 g/dm³, and increased the pH of both sandy and loam soils. Survival and persistence of the E. coli strains generally varied according to soil type, with strains generally surviving better (P ≤ 0.05) in loam soil compared to in sandy soil. In loam soil and biochar amended loam soils, E. coli strains remained culturable until the 150th day with counts ranging between 3.00 and 5.94 ± 0.04 log CFU/g. The effects of biochar on the physicochemical properties of soil and the response of the E. coli strains to biochar amendment was variable depending on soil type.

The impact of environmental factors on the transport and survival of pathogens in agricultural soils from karst areas of Yunnan province, China: Laboratory column simulated leaching experiments

Introduction

Groundwater is considered the best candidate for drinking water supply in the karst area. The groundwater water resources, however, are vulnerable to pathogenic microorganism contamination because of the typically thin soil layers overlying aquifers and the high permeability of the aquifer host rock, resulting in short residence times and low natural attenuation capacities. Until now, little attention has been paid to the critical environmental factors affecting the pathogenic microorganism contamination in soil-groundwater systems in the karst area.

Methods

In the study, orthogonality column experiments with controlling ambient temperatures, pH values of inlet water, and soil porosities were carried out to investigate the transport and lifespan of pathogenic microorganisms in the leachate of agricultural soils in the karst area of Yunnan province, China. The pathogenic indicators, i.e., total bacteria count (TBC) and total coliforms count (TCC), and hydrochemical parameters, i.e., pH and permanganate index (CODMn) in the leaching water, were systematically monitored.

Results and Discussion

The results showed that bacteria including coliforms can survive for prolonged periods of time in karst soils. The soils overlying the karst rocks were unable to impede the bacteria from seeping into the groundwater. The soils, in turn, likely served as both reservoirs and incubators for pathogenic bacteria. The ambient temperature was the most predominant influential factor affecting both TBC and TCC. The bacteria concentrations were proportional to the temperature in the leachate. Therefore, more attention should be paid to temperature variations in protecting the water supply, particularly in the high-temperature period, such as during the summer months.

Resilience of soil microbial metabolic functions to temporary E. coli invasion

Due to the globalization and increasing human activities, there is a significant increase in bacterial invasions to the soil ecosystems. Soil resident communities are vulnerable to bacterial invasion and suffered legacy effects after unsuccessful invasion. However, whether such changes in the soil ecosystems are permanent or temporary remains unclear. Here, we investigated the functional resilience of soil ecosystems to bacterial invasion and intensive managements. We used Escherichia coli O157:H7 (E. coli) as model strain examined the soil microbial metabolic functions, including enzyme activities, nitrogen and carbon use efficiency, community niche, and carbon metabolic potential, as well as soil physicochemical properties and microbial invader survival in 8 soil samples, 4 from natural hardwood forests and 4 from intensively managed Moso bamboo forests. The results showed that soil ecosystems were not resistant to E. coli invasion regardless of the intensity of management, which the finding was significantly reflected in the nutrient-acquiring activities or carbon utilization, or both. Besides, the invasion legacy effect (the effect after invader apoptosis) was positively related to E. coli survival time. However, most of the metabolic functions could recover almost to the initial state after 135 days of incubation, suggesting a strong recovery capacity of the soil ecosystems. These data indicate that E. coli invasion has a legacy effect on the functions of soil resident communities. However, soil ecosystems are highly resilient even under intensive human management.

What on earth? The impact of digestates and composts from farm effluent management on fluxes of foodborne pathogens in agricultural lands

The recycling of biomass is the cornerstone of sustainable development in the bioeconomy. In this context, digestates and composts from processed agricultural residues and biomasses are returned to the soil. Whether or not the presence of pathogenic microorganisms in these processed biomasses is a threat to the sustainability of the current on-farm practices is still the subject of debate. In this review, we describe the microbial pathogens that may be present in digestates and composts. We then provide an overview of the current European regulation designed to mitigate health hazards linked to the use of organic fertilisers and soil improvers produced from farm biomasses and residues. Finally, we discuss the many factors that underlie the fate of microbial pathogens in the field. We argue that incorporating land characteristics in the management of safety issues connected with the spreading of organic fertilisers and soil improvers can improve the sustainability of biomass recycling.

Persistence of E. coli O157:H7 in urban recreational waters from Spring and Autumn: a comparison analysis

People might get infected by pathogens found in urban recreational waters during water-contact activities, such as swimming, boating, bathing, and yachting. However, the persistence of pathogenic bacteria in those waters was not well documented. In this study, persistence of E. coli O157:H7 (EcO157) in 48 water samples (24 Spring samples and 24 Autumn samples) from the 3 urban recreational waters was investigated. Multivariate statistical analysis was performed to correlate survival data with water physicochemical properties and bacterial communities. Our data showed that EcO157 survived longer in Spring samples than in Autumn samples regardless of the lakes. Results revealed that recreational water physicochemical properties and bacterial community in Spring samples were different from those in Autumn samples. Mantel and Partial Mantel tests, as well as co-occurrence network analysis illustrated that EC salinity, TOC, and bacterial community were correlated with survival time (ttd) (p < 0.05). Variation partition analysis (VPA) indicated that bacterial community, EC, TOC, and TN explained about 64.81% of overall ttd variation in Spring samples, and bacterial community, EC, pH, and TP accounted for about 56.59% of overall ttd variation in Autumn samples. Structural equation model (SEM) illustrated that EC indirectly positively affected ttd through bacterial community. The correlation between bacterial community and ttd was negative in Spring samples and positive in Autumn samples. TN appeared a direct positive effect on ttd in Spring samples. TP displayed a direct negative effect on ttd in Autumn samples. Our results concluded that there was seasonal variation in environmental factors that directly or indirectly affected the survival of EcO157 in urban recreational waters.

Persistence of Salmonella Typhimurium in apple-pear (Pyrus bretschneideri Rehd.) orchard soils influenced by bacterial communities and soil properties

2In this study, we investigated the persistence of Salmonella Typhimurium in 26 soil samples from apple-pear orchards in Yanji, Longjing and Helong in northeastern China. The time to reach detection limit (ttds) of Salmonella Typhimurium in soils varied from 20 to 120 days. Redundancy analysis and variation partition analysis elucidated that bacterial communities, clay content, pH, electrical conductivity (EC) salinity, and NO₃^--N could explain more than 85% of overall variation of the persistence behaviors. Results of structural equation models and Mantel tests revealed that clay content and EC displayed both direct and indirect effect on ttds, while NO₃^--N and pH exhibited direct and indirect effect on the survival patterns, respectively. Furthermore, Actinobacteria, Acidobacteria and Deltaproteobacteria at class level showed highly close correlations with ttds. Our results revealed that certain biotic and abiotic factors could greatly contribute to the overall persistence of Salmonella in apple-pear orchard soils.

Soil salinity, pH, and indigenous bacterial community interactively influence the survival of E. coli O157:H7 revealed by multivariate statistics

Complexities of biotic-abiotic interactions in soils result in the lack of integrated understanding of environmental variables that restrict the survival of shiga toxin-producing E. coli O157:H7. Herein, we reanalyzed previously published data and highlighted the influence of soil abiotic factors on E. coli O157:H7 survivability and elucidated how these factors took effect indirectly through affecting indigenous bacterial community. Interaction network analysis indicated salinity and pH decreased the relative abundances of some bacterial taxa (e.g., Acidobacteria_Gp4, Acidobacteria_Gp6, and Deltaproteobacteria) which were positively correlated with the survival of E. coli O157:H7 in soils, and vice versa (e.g., Gammaproteobacteria and Flavobacteria) (P < 0.05). An array of multivariate statistical approaches including partial Mantel test, variation partition analysis (VPA), and structural equation model (SEM) further confirmed that biotic and abiotic factors interactively shaped the survival profile of E. coli O157:H7. This study revealed that some bacterial taxa were correlated with survival of E. coli O157:H7 directly, and salinity and pH could affect E. coli O157:H7 survival through changing these bacterial taxa. These findings suggest that salinity in soil might benefit the control of fecal pathogenic E. coli invasion, while soil acidification caused by anthropogenic influences could potentially increase the persistence of E. coli O157:H7 in agro-ecosystem.

Disentangling survival of Escherichia coli O157:H7 in soils: From a subpopulation perspective

Soil physicochemical properties and microbial community have been proved to be correlated to survival behaviors of Shiga toxin-producing Escherichia coli O157:H7, but the roles of biotic and abiotic factors in the different stages of inactivation process remain unclear. Here, fruit producing soils were collected, and soils physicochemical properties, bacterial and fungal community structure were characterized. Survival experiments were performed by inoculating E. coli O157:H7 in soils. Double Weibull survival model was found to better fit the experimental data, and two subpopulations with different capability on resistance to stress were identified. The sensitive subpopulation with smaller δ (time needed for first decimal reduction) (i.e., δ₁) died off faster compared to the more resistant subpopulation with greater δ (i.e., δ₂). Partial Mantel test revealed that ttd (time needed to reach detection limit) was jointly influenced by physical factors, chemical factors, and bacterial composition (P < 0.05); δ₁ was shaped by physical factors (P < 0.01) and additional bacterial composition (P < 0.05); and δ₂ was strongly steered by bacterial community (P < 0.001). Bacterial co-occurrence network analysis revealed that samples with lower δ₂ were coupled with higher network complexity and closer taxa relationship (e.g. higher average (weighted) degree, higher network diameter, higher graph density, and lower modularity), and vice versa. Taken together, the sensitive subpopulation had difficulty in adapting to coarse particles conditions, while resistant subpopulation might eventually succumb to the robust biodiversity. This study provides novel insights into the E. coli O157:H7 survival mechanism through subpopulation perspective and sheds light on the reduction of edaphic colonization by pathogens via agricultural management strategy.

A Predictive Model for Survival of Escherichia coli O157:H7 and Generic E. coli in Soil Amended with Untreated Animal Manure

This study aimed at developing a predictive model that captures the influences of a variety of agricultural and environmental variables and is able to predict the concentrations of enteric bacteria in soil amended with untreated Biological Soil Amendments of Animal Origin (BSAAO) under dynamic conditions. We developed and validated a Random Forest model using data from a longitudinal field study conducted in mid-Atlantic United States investigating the survival of Escherichia coli O157:H7 and generic E. coli in soils amended with untreated dairy manure, horse manure, or poultry litter. Amendment type, days of rain since the previous sampling day, and soil moisture content were identified as the most influential agricultural and environmental variables impacting concentrations of viable E. coli O157:H7 and generic E. coli recovered from amended soils. Our model results also indicated that E. coli O157:H7 and generic E. coli declined at similar rates in amended soils under dynamic field conditions.The Random Forest model accurately predicted changes in viable E. coli concentrations over time under different agricultural and environmental conditions. Our model also accurately characterized the variability of E. coli concentration in amended soil over time by providing upper and lower prediction bound estimates. Cross-validation results indicated that our model can be potentially generalized to other geographic regions and incorporated into a risk assessment for evaluating the risks associated with application of untreated BSAAO. Our model can be validated for other regions and predictive performance also can be enhanced when data sets from additional geographic regions become available.

Interaction between Fungal Communities, Soil Properties, and the Survival of Invading E. coli O157:H7 in Soils

Pathogens that invade into the soil cancontaminate food and water, andinfect animals and human beings. It is well documented that individual bacterial phyla are well correlated with the survival of E. coliO157 (EcO157), while the interaction betweenthe fungal communities and EcO157 survival remains largely unknown. In this study, soil samples from Tongliao, Siping, and Yanji in northeast China were collected and characterized. Total DNA was extracted for fungal and bacterial community characterization. EcO157 cells were spiked into the soils, and their survival behavior was investigated. Results showed that both fungal and bacterial communities were significantly correlated (p < 0.01) with the survival of EcO157 in soils, and the relative abundances of fungal groups (Dothideomycetes and Sordariomycetes) and some bacterial phyla (Acidobacteria, Firmicutes, gamma- and delta-Proteobacteria)weresignificantly correlated with ttds (p < 0.01). Soil pH, EC (electric conductance) salinity, and water-soluble nitrate nitrogen were significantly correlated with survival time (time to reach the detection limit, ttd) (p < 0.05). The structural equation model indicated that fungal communities could directly influence ttds, and soil properties could indirectly influence the ttds through fungal communities. The first log reduction time (δ) was mainly correlated with soil properties, while the shape parameter (p) was largely correlated with fungal communities. Our data indicated that both fungal and bacterial communities were closely correlated (p < 0.05)with the survival of EcO157 in soils, and different fungal and bacterial groups might play different roles. Fungal communities and bacterial communities explained 5.87% and 17.32% of the overall variation of survival parameters, respectively. Soil properties explained about one-third of the overall variation of survival parameters. These findings expand our current understanding of the environmental behavior of human pathogens in soils.

The response of nitrogen cycling and bacterial communities to E. coli invasion in aquatic environments with submerged vegetation

The effects of exogenous Escherichia coli on nitrogen cycling (N-cycling) in freshwater remains unclear. Thus, seven ecosystems, six with submerged plants-Potamogeton crispus (PC) and Myriophyllum aquaticum (MA)-and one with no plants were set up. Habitats were assessed before and after E. coli addition (10⁷ colony-forming units/mL). E. coli colonization of freshwater ecosystems had significant effects on bacterial community structure in plant surface biofilms and surface sediments (ANOVA, P < 0.05). It reduced the relative abundance of nitrosification bacteria (-70.94 ± 26.17%) and nitrifiers (-47.86 ± 23.68%) in biofilms which lead to significant reduction of ammoxidation in water (P < 0.05). The N-cycling intensity from PC systems was affected more strongly by E. coli than were MA systems. Furthermore, the coupling coefficient of exogenous E. coli to indigenous N-cycling bacteria in sediments (6.061, average connectivity degree) was significantly weaker than that in biofilms (9.852). Additionally, at the genus level, E. coli were most-closely associated with N-cycling bacteria such as Prosthecobacter, Hydrogenophaga, and Bacillus in sediments and biofilms according to co-occurrence bacterial network (Spearman). E. coli directly changed their abundance, so that the variability of species composition of N-cycling bacterial taxa was triggered, as well. Overall, exogenous E. coli repressed ammoxidation, but promoted ammonification and denitrification. Our results provided new insights into how pathogens influence the nitrogen cycle in freshwater ecosystems.

Are we overestimating risk of enteric pathogen spillover from wild birds to humans?

Enteric illnesses remain the second largest source of communicable diseases worldwide, and wild birds are suspected sources for human infection. This has led to efforts to reduce pathogen spillover through deterrence of wildlife and removal of wildlife habitat, particularly within farming systems, which can compromise conservation efforts and the ecosystem services wild birds provide. Further, Salmonella spp. are a significant cause of avian mortality, leading to additional conservation concerns. Despite numerous studies of enteric bacteria in wild birds and policies to discourage birds from food systems, we lack a comprehensive understanding of wild bird involvement in transmission of enteric bacteria to humans. Here, we propose a framework for understanding spillover of enteric pathogens from wild birds to humans, which includes pathogen acquisition, reservoir competence and bacterial shedding, contact with people and food, and pathogen survival in the environment. We place the literature into this framework to identify important knowledge gaps. Second, we conduct a meta‐analysis of prevalence data for three human enteric pathogens, Campylobacter spp., E. coli, and Salmonella spp., in 431 North American breeding bird species. Our literature review revealed that only 3% of studies addressed the complete system of pathogen transmission. In our meta‐analysis, we found a Campylobacter spp. prevalence of 27% across wild birds, while prevalence estimates of pathogenic E. coli (20%) and Salmonella spp. (6.4%) were lower. There was significant bias in which bird species have been tested, with most studies focusing on a small number of taxa that are common near people (e.g. European starlings Sturnus vulgaris and rock pigeons Columba livia) or commonly in contact with human waste (e.g. gulls). No pathogen prevalence data were available for 65% of North American breeding bird species, including many commonly in contact with humans (e.g. black‐billed magpie Pica hudsonia and great blue heron Ardea herodias), and our metadata suggest that some under‐studied species, taxonomic groups, and guilds may represent equivalent or greater risk to human infection than heavily studied species. We conclude that current data do not provide sufficient information to determine the likelihood of enteric pathogen spillover from wild birds to humans and thus preclude management solutions. The primary focus in the literature on pathogen prevalence likely overestimates the probability of enteric pathogen spillover from wild birds to humans because a pathogen must survive long enough at an infectious dose and be a strain that is able to colonize humans to cause infection. We propose that future research should focus on the large number of under‐studied species commonly in contact with people and food production and demonstrate shedding of bacterial strains pathogenic to humans into the environment where people may contact them. Finally, studies assessing the duration and intensity of bacterial shedding and survival of bacteria in the environment in bird faeces will help provide crucial missing information necessary to calculate spillover probability. Addressing these essential knowledge gaps will support policy to reduce enteric pathogen spillover to humans and enhance bird conservation efforts that are currently undermined by unsupported fears of pathogen spillover from wild birds.

Sediment pH, not the bacterial diversity, determines Escherichia coli O157:H7 survival in estuarine sediments

Shiga toxin-producing Escherichia coli (E. coli) O157:H7 is recognized as a hazardous microorganism in the environment. Its longer survival might contribute to higher contamination risk. In this study, E. coli O157:H7 survival in estuarine sediments collected from south Hangzhou Bay was investigated. The survival time of E. coli O157:H7 in estuarine sediments increased with the distance to the water-land junction. Sediment pH was the most important factor in regulating E. coli O157:H7 survival in estuarine sediments. In addition, sediment nutrients and texture also played significant roles in the survival of E. coli O157:H7 in the sediments. On the other hand, bacterial diversity as determined by the alpha-diversity index had no significant effect on E. coli O157:H7 survival. However, specific families of bacteria were closely associated with E. coli O157:H7 survival in the sediments. Remarkably, some potential bacterial groups, e.g., the Desulfobacteraceae, Desulfobulbaceae and Desulfarculaceae families, which are mainly involved in the sulfur cycle, showed significant negative correlation with the E. coli O157:H7 survival in the sediments. On the whole, abiotic factors showed greater effects on E. coli O157:H7 survival in the test sediments than the bacterial community. Our findings provide a comprehensive understanding of E. coli O157:H7 survival and regulatory factors in estuarine sediments, establishing foundation for the prevention of pathogen contamination.

Fate of Labile Organic Carbon in Paddy Soil Is Regulated by Microbial Ferric Iron Reduction

Global paddy soil is the primary source of methane, a potent greenhouse gas. It is therefore highly important to understand the carbon cycling in paddy soil. Microbial reduction of iron, which is widely found in paddy soil, is likely coupled with the oxidation of dissolved organic matter (DOM) and suppresses methanogenesis. However, little is known about the biotransformation of small molecular DOM accumulated under flooded conditions and the effect of iron reduction on the biotransformation pathway. Here, we carried out anaerobic incubation experiments using field-collected samples amended with ferrihydrite and different short-chain fatty acids. Our results showed that less than 20% of short-chain fatty acids were mineralized and released to the atmosphere. Using Fourier transform ion cyclotron resonance mass spectrometry, we further found that a large number of recalcitrant molecules were produced during microbial consumption of these short-chain fatty acids. Moreover, the biotransformation efficiency of short-chain fatty acids decreased with the increasing length of carbon chains. Ferrihydrite addition promoted microbial assimilation of short-chain fatty acids as well as enhanced the activation and biotransformation of indigenous stable carbon in the soil replenished with formate. This study demonstrates the significance of ferrihydrite in the biotransformation of labile DOM and promotes a more comprehensive understanding of the coupling of iron reduction and carbon cycling in paddy soils.

Effects of Cultivating Years on Survival of Culturable Escherichia coli O157:H7 in Greenhouse Soils

The extent to how Escherichia coli O157:H7 can survive in soil and the predominant factors that determine its survival are crucial issues from a public health point of view. This study investigated the survival of E. coli O157:H7 in vegetable soils in plastic-greenhouse cultivation over 0, 1, 4, 8, and 12 years in southern China. Results showed that the survival times ( t_d) calculated from the Weibull model for the five tested soils ranged from 9.00 to 21.11 days. In general, E. coli O157:H7 survived longer in open-field soils than in greenhouse soils under the same incubation conditions. The t_d values were greater in soils with a lower level of electrical conductivity, a higher level of total nitrogen, and a higher level of sand content. Compared to other factors, electrical conductivity was the most important factor affecting the survival of E. coli O157:H7 in the tested soils. Different survival times of E. coli O157:H7 in vegetable soils under diverse cultivation patterns highlight the importance of preventing pathogenic contamination for the purpose of food safety.

Comparative persistence of Salmonella and Escherichia coli O157:H7 in loam or sandy loam soil amended with bovine or swine manure

The fate of Salmonella and Escherichia coli O157:H7 in swine or dairy manure amended into sandy loam or loam soil under field conditions was studied. Soil was amended with manure inoculated with a Salmonella or E. coli O157:H7 cocktail, then transferred to 0.22 μm pore size membrane walled vials. The vials were then placed on the surface or at 15 cm depth in the test plots. Pathogen numbers, soil moisture, rainfall, and temperature were measured throughout the three trials (20-47 weeks duration) representing spring or fall application. Survival curves were characterized by having an initial rapid decline in pathogen numbers followed by a slower inactivation phase with an occasional increase in culturable cells. The CT_99.9 values (time to reach a 3 log CFU reduction) varied from 2 to 120 days, with the most rapid decrease being observed on the surface of sandy loam soil. The persistence of pathogens is primarily governed by variations in moisture and temperature, although season of application along with manure and soil type also contribute. To generate more accurate predictive pathogen models, there is a need for laboratory-based trials to mirror the dynamic variation in temperature and soil moisture encountered within the natural environment.

Vertical variation of a black soil's properties in response to freeze-thaw cycles and its links to shift of microbial community structure

Soil freeze-thaw cycles (FTCs) change soil physical, chemical, and biological properties, however information regarding their vertical variations in response to FTCs is limited. In this work, black soil (silty loam) packed soil columns were exposed to 8 FTCs, and soil properties were determined for each of vertical layer of soil columns. The results revealed that after FTCs treatment, moisture and electrical conductivity (EC) salinity tended to increase in upper soil layers. Increments of ammonium nitrogen (NH₄⁺-N) and nitrate nitrogen (NO₃^--N) in top layers (0-10cm) were greater than those in other layers, and increments of water soluble organic carbon (WSOC) and decrease of microbial biomass carbon (MBC) in middle layers (10-20cm) were greater than those in both ends. Overall, microbial community structure was mainly influenced by soil physical properties (moisture and EC) and chemical properties (pH and WSOC). For bacterial (archaeal) and fungal communities, soil physical properties, chemical properties and their interaction explained 79.73% and 82.66% of total variation, respectively. Our results provided insights into the vertical variation of soil properties caused by FTCs, and such variation had a major impact on the change of structure and composition of soil bacterial and fungal communities.

Persistence of Salmonella Typhimurium in Well Waters from a Rural Area of Changchun City, China

Salmonella-contaminated well water could cause major infection outbreaks worldwide, thus, it is crucial to understand their persistence in those waters. In this study, we investigated the persistence of Salmonella enterica serovar Typhimurium in 15 well waters from a rural area of Changchun City, China. Results illustrated that the time to reach detection limit (ttd), first decimal reduction time (δ), and the shape parameter (p) ranged from 15 to 80 days, from 5.6 to 66.9 days, and from 0.6 to 6.6, respectively. Principal component analysis showed that ttds of S. Typhimurium were positively correlated with total organic carbon, pH, NH₄⁺–N, and total phosphate. Multiple stepwise regression analysis revealed that ttds could be best predicted by NH₄⁺–N and pH. Canonical correspondence analysis and variation partition analysis revealed that NH₄⁺–N and pH, and the rest of the water parameters, could explain 27.60% and 28.15% of overall variation of the survival behavior, respectively. In addition, ttds were found to be correlated (p < 0.01) with δ and p. Our results showed that the longer survival (>2.5 months) S. Typhimurium could constitute an increased health risk to the local communities, and provided insights into the close linkage between well water quality and survival of S. Typhimurium.

Exploring links between water quality and E. coli O157:H7 survival potential in well waters from a rural area of southern Changchun City, China

Waterborne infectious disease outbreak associated with well water contamination is a worldwide public health issue, especially for rural areas in developing countries. In the current study, we characterized 20 well water samples collected from a rural area of southern Changchun city, China, and investigated the survival potential of Escherichia coli O157:H7 in those water samples. The results showed that nitrate and ammonia concentrations in some well water samples exceed the corresponding China drinking water standards, indicating potential contamination by local agricultural farms. Our results also revealed that the average survival time (ttd) of E. coli O157:H7 in all well water samples was 30.09 days, with shortest and longest ttd being 17.95 and 58.10 days, respectively. The ttds were significantly correlated with pH and the ratio of total nitrogen to total phosphorus. In addition, it was found that the shape parameter (p) and first decimal reduction parameter (δ) were negatively (P < 0.05) and positively (P < 0.05) correlated to ttd, respectively. Our study showed that E. coli O157:H7 could survive up to two months in well water, suggesting that this pathogen could constitute a great public health risk.

Field Evidence Supporting Conventional Onion Curing Practices as a Strategy To Mitigate Escherichia coli Contamination from Irrigation Water

The Produce Safety Rule of the U.S. Food Safety Modernization Act includes restrictions on the use of agricultural water of poor microbiological quality. Mitigation options for poor water quality include the application of an irrigation-to-harvest interval of <4 days; however, dry bulb onion production includes an extended irrigation-to-harvest interval (<30 days). This study evaluated conventional curing practices for mitigating Escherichia coli contamination in a field setting. Well water inoculated with rifampin-resistant E. coli (1, 2, or 3 log CFU/mL) was applied to onion fields (randomized block design; n = 5) via drip tape on the final day of irrigation. Onions remained undisturbed for 7 days and were then lifted to the surface to cure for an additional 21 days before harvest. Water, onions, and soil were tested for presence of rifampin-resistant E. coli. One day after irrigation, 13.3% of onions (20 of 150) receiving the poorest quality water (3 log CFU/mL) tested positive for E. coli; this prevalence was reduced to 4% (6 of 150 onions) after 7 days. Regardless of inoculum level, E. coli was not detected on any onions beyond 15 days postirrigation. These results support conventional dry bulb onion curing practices as an effective strategy to mitigate microbiological concerns associated with poor quality irrigation water.

Variations of Escherichia coli O157:H7 Survival in Purple Soils

Escherichia coli O157:H7 is a well-recognized cause of human illness. Survival of Escherichia coli O157:H7 in five purple soils from Sichuan Province was investigated. The dynamics of E. coli O157:H7 survival in purple soils were described by the Weibull model. Results showed that this model is suitable to fit survival curves of E. coli O157:H7 in purple soils, with the calculated td value (survival time needed to reach the detection limit of 100 CFU·g-1) ranging from 2.99 days to 26.36 days. The longest survival time of E. coli O157:H7 was observed in neutral purple soils (24.49 days), followed by alkalescent purple soil (18.62 days) and acid purple soil (3.48 days). The redundancy analysis (RDA) revealed that td values were significantly enhanced by soil nutrition (total organic carbon (OC), total nitrogen (TN), available potassium (AK) and the ratio of humic acid to fulvic acid (Ha/Fa)), but were significantly suppressed by iron and aluminum oxide.

Seasonal induced changes in spinach rhizosphere microbial community structure with varying salinity and drought

Salinity is a common problem under irrigated agriculture, especially in low rainfall and high evaporative demand areas of southwestern United States and other semi-arid regions around the world. However, studies on salinity effects on soil microbial communities are relatively few while the effects of irrigation-induced salinity on soil chemical and physical properties and plant growth are well documented. In this study, we examined the effects of salinity, temperature, and temporal variability on soil and rhizosphere microbial communities in sand tanks irrigated with prepared solutions designed to simulate saline wastewater. Three sets of experiments with spinach (Spinacia oleracea L., cv. Racoon) were conducted under saline water during different time periods (early winter, late spring, and early summer). Bacterial 16S V4 rDNA region was amplified utilizing fusion primers designed against the surrounding conserved regions using MiSeq® Illumina sequencing platform. Across the two sample types, bacteria were relatively dominant among three phyla-the Proteobacteria, Cyanobacteria, and Bacteroidetes-accounted for 77.1% of taxa detected in the rhizosphere, while Proteobacteria, Bacteroidetes, and Actinobacteria accounted for 55.1% of taxa detected in soil. The results were analyzed using UniFrac coupled with principal coordinate analysis (PCoA) to compare diversity, abundance, community structure, and specific bacterial groups in soil and rhizosphere samples. Permutational analysis of variance (PERMANOVA) analysis showed that soil temperature (P=0.001), rhizosphere temperature (P=0.001), rhizosphere salinity (P=0.032), and evapotranspiration (P=0.002) significantly affected beta diversity of soil and rhizosphere microbial communities. Furthermore, salinity had marginal effects (P=0.078) on soil beta diversity. However, temporal variability differentially affected rhizosphere microbial communities irrigated with saline wastewater. Therefore, microbial communities in soils impacted by saline irrigation water respond differently to irrigation water quality and season of application due to temporal effects associated with temperature.

A System Model for Understanding the Role of Animal Feces as a Route of Contamination of Leafy Greens before Harvest

The majority of foodborne outbreaks in the United States associated with the consumption of leafy greens contaminated with Escherichia coli O157:H7 have been reported during the period of July to November. A dynamic system model consisting of subsystems and inputs to the system (soil, irrigation, cattle, wild pig, and rainfall) simulating a hypothetical farm was developed. The model assumed two crops of lettuce in a year and simulated planting, irrigation, harvesting, ground preparation for the new crop, contamination of soil and plants, and survival of E. coli O157:H7. As predicted by the baseline model for crops harvested in different months from conventional fields, an estimated 13 out of 257 (5.05%) first crops harvested in July would have at least one plant with at least 1 CFU of E. coli O157:H7. Predictions indicate that no first crops would be contaminated with at least 1 CFU of E. coli O157:H7 for other months (April to June). The maximum E. coli O157:H7 concentration in a plant was higher in the second crop (27.10 CFU) than in the first crop (9.82 CFU). For the second crop, the probabilities of having at least one plant with at least 1 CFU of E. coli O157:H7 in a crop were predicted as 15/228 (6.6%), 5/333 (1.5%), 14/324 (4.3%), and 6/115 (5.2%) in August, September, October, and November, respectively. For organic fields, the probabilities of having at least one plant with ≥1 CFU of E. coli O157:H7 in a crop (3.45%) were predicted to be higher than those for the conventional fields (2.15%).

IMPORTANCE

This study is the first attempt toward developing a mathematical system model to understand the pathway of E. coli O157:H7 in the production of leafy greens. Results of the presented system model indicate that the seasonality of outbreaks of E. coli O157:H7-associated contamination of leafy greens was in good agreement with the prevalence of this pathogen in cattle and wild pig feces in a major leafy greens-producing region in California. On the basis of comparisons among the results of different scenarios, it can be recommended that the concentration of E. coli O157:H7 in leafy greens can be reduced considerably if contamination of soil with wild pig and cattle feces is mitigated.

Bacterial diversity and composition in major fresh produce growing soils affected by physiochemical properties and geographic locations

Microbial diversity of agricultural soils has been well documented, but information on leafy green producing soils is limited. In this study, we investigated microbial diversity and community structures in 32 (16 organic, 16 conventionally managed soils) from California (CA) and Arizona (AZ) using pyrosequencing, and identified factors affecting bacterial composition. Results of detrended correspondence analysis (DCA) and dissimilarity analysis showed that bacterial community structures of conventionally managed soils were similar to that of organically managed soils; while the bacterial community structures in soils from Salinas, California were different (P<0.05) from those in soils from Yuma, Arizona and Imperial Valley, California. Canonical correspondence analysis (CCA) and artificial neural network (ANN) analysis of bacterial community structures and soil variables showed that electrical conductivity (EC), clay content, water-holding capacity (WHC), pH, total nitrogen (TN), and organic carbon (OC) significantly (P<0.05) correlated with microbial communities. CCA based variation partitioning analysis (VPA) showed that soil physical properties (clay, EC, and WHC), soil chemical variables (pH, TN, and OC) and sampling location explained 16.3%, 12.5%, and 50.9%, respectively, of total variations in bacterial community structure, leaving 13% of the total variation unexplained. Our current study showed that bacterial community composition and diversity in major fresh produce growing soils from California and Arizona is a function of soil physiochemical characteristics and geographic distances of sampling sites.

Multistate Evaluation of Microbial Water and Sediment Quality from Agricultural Recovery Basins

Agricultural recovery basins are an important conservation practice designed to provide temporary storage of sediment and water on farms before low-volume discharge. However, food safety concerns have been raised regarding redistribution of captured sediment and water to fields used for human food production. The purpose of this study was to examine the potential microbiological risk that recovery basins may contribute to nearby produce fields and to evaluate characteristics that may influence or mitigate those risks. Water and sediment samples were collected from participating farms in three states and evaluated for bacterial indicators and pathogens over several months. Overall, 45% ( = 48) of water samples and less than 15% ( = 13) of sediment samples were positive for spp. In water samples, the occurrence of was positively associated with the use of surface water as a source of irrigation compared with groundwater as well as log-scale increases in concentration. In sediment samples, was associated with basin location (region) and basin fill levels. Sediment exposed to drying during dewatering had lower concentrations of indicator and a lower proportion of positives than submerged sediment from the same pond. Surrounding landscape characteristics, including vegetative coverage, proximity to livestock operations, and evidence of wildlife, were not correlated with pathogen occurrence in either sediment or water samples, suggesting that although habitat surrounding ponds may be an attractant to wildlife, those features may not contribute to increased pathogen occurrence in agricultural recovery basins.

Fate of Escherichia coli O157: H7 in agricultural soils amended with different organic fertilizers

Five organic fertilizers (vermicompost, pig manure, chicken manure, peat and oil residue) were applied to agricultural soils to study their effects on the survival of Escherichia coli O157:H7 (E. coli O157:H7). Results showed that E. coli O157:H7 survival changed greatly after organic fertilizers application, with shorter td values (survival time needed to reach the detection limit of 100 CFU g(-1)) (12.57±6.57 days) in soils amended with chicken manure and the longest (25.65±7.12 days) in soils amended with pig manure. Soil pH, EC and free Fe/Al (hydro) oxides were significant explanatory factors for E. coli O157:H7 survival in the original soils. Soil constituents (minerals and organic matter) and changes in their surface charges with pH increased the effect of soil pH on E. coli O157:H7 survival. However, electrical conductivity played a more important role in regulating E. coli O157:H7 survival in fertilizer-amended soils. This study highlighted the importance of choosing appropriate organic fertilizers in the preharvest environment to reduce food-borne bacterial contamination.

Persistence of Pathogenic and Non-Pathogenic Escherichia coli Strains in Various Tropical Agricultural Soils of India

The persistence of Shiga-like toxin producing E. coli (STEC) strains in the agricultural soil creates serious threat to human health through fresh vegetables growing on them. However, the survival of STEC strains in Indian tropical soils is not yet understood thoroughly. Additionally how the survival of STEC strain in soil diverges with non-pathogenic and genetically modified E. coli strains is also not yet assessed. Hence in the present study, the survival pattern of STEC strain (O157-TNAU) was compared with non-pathogenic (MTCC433) and genetically modified (DH5α) strains on different tropical agricultural soils and on a vegetable growing medium, cocopeat under controlled condition. The survival pattern clearly discriminated DH5α from MTCC433 and O157-TNAU, which had shorter life (40 days) than those compared (60 days). Similarly, among the soils assessed, the red laterite and tropical latosol supported longer survival of O157-TNAU and MTCC433 as compared to wetland and black cotton soils. In cocopeat, O157 recorded significantly longer survival than other two strains. The survival data were successfully analyzed using Double-Weibull model and the modeling parameters were correlated with soil physico-chemical and biological properties using principal component analysis (PCA). The PCA of all the three strains revealed that pH, microbial biomass carbon, dehydrogenase activity and available N and P contents of the soil decided the survival of E. coli strains in those soils and cocopeat. The present research work suggests that the survival of O157 differs in tropical Indian soils due to varied physico-chemical and biological properties and the survival is much shorter than those reported in temperate soils. As the survival pattern of non-pathogenic strain, MTCC433 is similar to O157-TNAU in tropical soils, the former can be used as safe model organism for open field studies.

Environmental monitoring of bacterial contamination and antibiotic resistance patterns of the fecal coliforms isolated from Cauvery River, a major drinking water source in Karnataka, India

The present study focuses prudent elucidation of microbial pollution and antibiotic sensitivity profiling of the fecal coliforms isolated from River Cauvery, a major drinking water source in Karnataka, India. Water samples were collected from ten hotspots during the year 2011-2012. The physiochemical characteristics and microbial count of water samples collected from most of the hotspots exhibited greater biological oxygen demand and bacterial count especially coliforms in comparison with control samples (p ≤ 0.01). The antibiotic sensitivity testing was performed using 48 antibiotics against the bacterial isolates by disk-diffusion assay. The current study showed that out of 848 bacterial isolates, 93.51% (n = 793) of the isolates were found to be multidrug-resistant to most of the current generation antibiotics. Among the major isolates, 96.46% (n = 273) of the isolates were found to be multidrug-resistant to 30 antibiotics and they were identified to be Escherichia coli by 16S rDNA gene sequencing. Similarly, 93.85% (n = 107), 94.49% (n = 103), and 90.22% (n = 157) of the isolates exhibited multiple drug resistance to 32, 40, and 37 antibiotics, and they were identified to be Enterobacter cloacae, Pseudomonas trivialis, and Shigella sonnei, respectively. The molecular studies suggested the prevalence of bla TEM genes in all the four isolates and dhfr gene in Escherichia coli and Sh. sonnei. Analogously, most of the other Gram-negative bacteria were found to be multidrug-resistant and the Gram-positive bacteria, Staphylococcus spp. isolated from the water samples were found to be methicillin and vancomycin-resistant Staphylococcus aureus. This is probably the first study elucidating the bacterial pollution and antibiotic sensitivity profiling of fecal coliforms isolated from River Cauvery, Karnataka, India.

Effects of climate change on the persistence and dispersal of foodborne bacterial pathogens in the outdoor environment: A review

According to the Intergovernmental Panel on Climate Change (IPCC), warming of the climate system is unequivocal. Over the coming century, warming trends such as increased duration and frequency of heat waves and hot extremes are expected in some areas, as well as increased intensity of some storm systems. Climate-induced trends will impact the persistence and dispersal of foodborne pathogens in myriad ways, especially for environmentally ubiquitous and/or zoonotic microorganisms. Animal hosts of foodborne pathogens are also expected to be impacted by climate change through the introduction of increased physiological stress and, in some cases, altered geographic ranges and seasonality. This review article examines the effects of climatic factors, such as temperature, rainfall, drought and wind, on the environmental dispersal and persistence of bacterial foodborne pathogens, namely, Bacillus cereus, Brucella, Campylobacter, Clostridium, Escherichia coli, Listeria monocytogenes, Salmonella, Staphylococcus aureus, Vibrio and Yersinia enterocolitica. These relationships are then used to predict how future climatic changes will impact the activity of these microorganisms in the outdoor environment and associated food safety issues. The development of predictive models that quantify these complex relationships will also be discussed, as well as the potential impacts of climate change on transmission of foodborne disease from animal hosts.

Effect of the food production chain from farm practices to vegetable processing on outbreak incidence

The popularity in the consumption of fresh and fresh-cut vegetables continues to increase globally. Fresh vegetables are an integral part of a healthy diet, providing vitamins, minerals, antioxidants and other health-promoting compounds. The diversity of fresh vegetables and packaging formats (spring mix in clamshell container, bagged heads of lettuce) support increased consumption. Unfortunately, vegetable production and processing practices are not sufficient to ensure complete microbial safety. This review highlights a few specific areas that require greater attention and research. Selected outbreaks are presented to emphasize the need for science-based 'best practices'. Laboratory and field studies have focused on inactivation of pathogens associated with manure in liquid, slurry or solid forms. As production practices change, other forms and types of soil amendments are being used more prevalently. Information regarding the microbial safety of fish emulsion and pellet form of manure is limited. The topic of global climate change is controversial, but the potential effect on agriculture cannot be ignored. Changes in temperature, precipitation, humidity and wind can impact crops and the microorganisms that are associated with production environments. Climate change could potentially enhance the ability of pathogens to survive and persist in soil, water and crops, increasing human health risks. Limited research has focused on the prevalence and behaviour of viruses in pre and post-harvest environments and on vegetable commodities. Globally, viruses are a major cause of foodborne illnesses, but are seldom tested for in soil, soil amendments, manure and crops. Greater attention must also be given to the improvement in the microbial quality of seeds used in sprout production. Human pathogens associated with seeds can result in contamination of sprouts intended for human consumption, even when all appropriate 'best practices' are used by sprout growers.

Topological data analysis of Escherichia coli O157:H7 and non-O157 survival in soils

Shiga toxin-producing E. coli O157:H7 and non-O157 have been implicated in many foodborne illnesses caused by the consumption of contaminated fresh produce. However, data on their persistence in soils are limited due to the complexity in datasets generated from different environmental variables and bacterial taxa. There is a continuing need to distinguish the various environmental variables and different bacterial groups to understand the relationships among these factors and the pathogen survival. Using an approach called Topological Data Analysis (TDA); we reconstructed the relationship structure of E. coli O157 and non-O157 survival in 32 soils (16 organic and 16 conventionally managed soils) from California (CA) and Arizona (AZ) with a multi-resolution output. In our study, we took a community approach based on total soil microbiome to study community level survival and examining the network of the community as a whole and the relationship between its topology and biological processes. TDA produces a geometric representation of complex data sets. Network analysis showed that Shiga toxin negative strain E. coli O157:H7 4554 survived significantly longer in comparison to E. coli O157:H7 EDL 933, while the survival time of E. coli O157:NM was comparable to that of E. coli O157:H7 EDL 933 in all of the tested soils. Two non-O157 strains, E. coli O26:H11 and E. coli O103:H2 survived much longer than E. coli O91:H21 and the three strains of E. coli O157. We show that there are complex interactions between E. coli strain survival, microbial community structures, and soil parameters.

Persistence of Escherichia coli O157 and non-O157 strains in agricultural soils

Shiga toxin producing Escherichia coli O157 and non-O157 serogroups are known to cause serious diseases in human. However, research on the persistence of E. coli non-O157 serogroups in preharvest environment is limited. In the current study, we compared the survival behavior of E. coli O157 to that of non-O157 E. coli strains in agricultural soils collected from three major fresh produce growing areas of California (CA) and Arizona (AZ). Results showed that the nonpathogenic E. coli O157:H7 4554 survived longer than the pathogenic E. coli O157:H7 EDL933 in Imperial Valley CA and Yuma AZ, but not in soils from the Salinas area. However, E. coli O157:NM was found to persist significantly longer than E. coli O157:H7 EDL933 in all soil tested from the three regions. Furthermore, two non-O157 (E. coli O26:H21 and E. coli O103:H2) survived significantly longer than E. coli O157:H7 EDL933 in all soils tested. Pearson correlation analysis showed that survival of the E. coli strains was affected by different environmental factors. Our data suggest that survival of E. coli O157 and non-O157 may be strain and soil specific, and therefore, care must be taken in data interpretation with respect to survival of this pathogen in different soils.

Internalization and fate of Escherichia coli O157:H7 in leafy green phyllosphere tissue using various spray conditions

In the past decade, leafy greens have been implicated in several outbreaks of foodborne illness, and research has focused on contamination during preharvest operations. Concerns have been raised that internalization of pathogens into the edible tissue occurs where postharvest chemical interventions would be ineffective. This study was initiated to measure the degree and fate of Escherichia coli O157:H7 internalized in the phyllosphere tissue of leafy greens when spray conditions, inoculum level, and type of leafy green were varied. Two spraying treatments were applied: (i) spraying individual spinach or lettuce leaves on plants once with a high dose (7 to 8 log CFU/ml) of E. coli O157:H7 and (ii) spraying spinach, lettuce, or parsley plants repeatedly (once per minute) with a low dose (2.7 to 4.2 log CFU/ml) of E. coli O157:H7 over a 10- to 20-min period. With the high-dose spray protocol, no significant differences in the prevalence of internalization occurred between Shiga toxin-negative E. coli O157:H7 isolates and virulent isolates (P > 0.05), implying that the Shiga toxin virulence factors did not influence internalization or the subsequent fate of those populations under these test conditions. Significantly greater internalization of E. coli O157:H7 occurred in spinach leaves compared with lettuce leaves when leaves were sprayed once with the high-dose inoculum (P < 0.05), whereas internalization was not observed in lettuce leaves but continued to be observed in spinach and parsley leaves following repeated spraying of the low-dose inoculum. Based on these results, it is surmised that a moisture film was generated when spraying was repeated and this film assisted in the mobilization of pathogen cells to plant apertures, such as stomata. E. coli O157:H7 cells that were internalized into spinach tissue using a low-dose repeat-spray protocol were temporary residents because they were not detected 2 days later, suggesting that plant-microbe interactions may be responsible.

Survival of Escherichia coli O157:H7 in soils under different land use types

Laboratory studies on Escherichia coli O157:H7 survival in soils from four different land use types: forest, tea plantation, bamboo grove, and vegetable garden were investigated at 25 ± 1 °C with the field capacity (soil water content at -33 kPa). Results showed that E. coli O157:H7 declined quickly in the test soils, but its survival dynamics varied in the soils under different land use types. The survival time needed to reach the detection limit (t d) in the test soils ranged from 2.1 to 3.6 days, with slightly longer t d values being observed in soils from the bamboo grove. Stepwise multiple regression analysis revealed that the t d values were shorter in sandy, lower pH, and lower organic carbon content soils. Different E. coli O157:H7 survival time in the soils under different land uses suggests that it is important to adapt proper management practices for reducing the potential risks of pathogen contamination when diary manure is applied to agricultural land.

Survival of Escherichia coli O157:H7 in soils from Jiangsu Province, China

Escherichia coli O157:H7 (E. coli O157:H7) is recognized as a hazardous microorganism in the environment and for public health. The E. coli O157:H7 survival dynamics were investigated in 12 representative soils from Jiangsu Province, where the largest E. coli O157:H7 infection in China occurred. It was observed that E. coli O157:H7 declined rapidly in acidic soils (pH, 4.57 – 5.14) but slowly in neutral soils (pH, 6.51 – 7.39). The survival dynamics were well described by the Weibull model, with the calculated t_d value (survival time of the culturable E. coli O157:H7 needed to reach the detection limit of 100 CFU g⁻¹) from 4.57 days in an acidic soil (pH, 4.57) to 34.34 days in a neutral soil (pH, 6.77). Stepwise multiple regression analysis indicated that soil pH and soil organic carbon favored E. coli O157:H7 survival, while a high initial ratio of Gram-negative bacteria phospholipid fatty acids (PLFAs) to Gram-positive bacteria PLFAs, and high content of exchangeable potassium inhibited E. coli O157:H7 survival. Principal component analysis clearly showed that the survival profiles in soils with high pH were different from those with low pH.

Microbial diversity and structure are drivers of the biological barrier effect against Listeria monocytogenes in soil

Understanding the ecology of pathogenic organisms is important in order to monitor their transmission in the environment and the related health hazards. We investigated the relationship between soil microbial diversity and the barrier effect against Listeria monocytogenes invasion. By using a dilution-to-extinction approach, we analysed the consequence of eroding microbial diversity on L. monocytogenes population dynamics under standardised conditions of abiotic parameters and microbial abundance in soil microcosms. We demonstrated that highly diverse soil microbial communities act as a biological barrier against L. monocytogenes invasion and that phylogenetic composition of the community also has to be considered. This suggests that erosion of diversity may have damaging effects regarding circulation of pathogenic microorganisms in the environment.

Primary isolation of shiga toxigenic from environmental sources

Since the time of the first microbe hunters, primary culture and isolation of bacteria has been a foundation of microbiology. Like other microbial methods, bacterial culture and isolation methodologies continue to develop. Although fundamental concepts like selection and enrichment are as relevant today as they were over 100 yr ago, advances in chemistry, molecular biology and bacterial ecology mean that today's culture and isolation techniques serve additional supporting roles. The primary isolation of Shiga toxigenic (STEC) from environmental sources relies on enriching the target while excluding extensive background flora. Due to the complexity of environmental substrates, no single method can be recommended; however, common themes are discussed. Brilliant Green Bile Broth, with or without antibiotics, is one of many broths used successfully for selective STEC enrichment. Stressed cells may require a pre-enrichment recovery step in a nonselective broth such as buffered peptone water. After enrichment, immunomagnetic separation with serotype specific beads drastically increases the chances for recovery of STEC from environmental or insect sources. Some evidence suggests that acid treating the recovered beads can further enhance isolation. Although it is common in human clinical, food safety, and water quality applications to plate the recovered beads on Sorbitol MacConkey Agar, other chromogenic media, such as modified CHROMagar, have proven helpful in field and outbreak applications, allowing the target to be distinguished from the numerous background flora. Optimum conditions for each sample and target must be determined empirically, highlighting the need for a better understanding of STEC ecology.

A framework for developing research protocols for evaluation of microbial hazards and controls during production that pertain to the application of untreated soil amendments of animal origin on land used to grow produce that may be consumed raw

Application of manure or soil amendments of animal origin (untreated soil amendments; UTSAs) to agricultural land has been a long-standing practice to maintain or improve soil quality through addition of organic matter, nitrogen, and phosphorus. Much smaller quantities of these types of UTSAs are applied to land used for food crops than to land used for animal grain and forage. UTSAs can harbor zoonotic enteric pathogens that may survive for extended periods after application. Additional studies are needed to enhance our understanding of preharvest microbial food safety hazards and control measures pertaining to the application of UTSAs especially for land used to grow produce that may be consumed raw. This document is intended to provide an approach to study design and a framework for defining the scope and type of data required. This document also provides a tool for evaluating the strength of existing data and thus can aid the produce industry and regulatory authorities in identifying additional research needs. Ultimately, this framework provides a means by which researchers can increase consistency among and between studies and facilitates direct comparison of hazards and efficacy of controls applied to different regions, conditions, and practices.